Dissertation Information for Manami Roychowdhury-SahaNAME:
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SCHOOL: ADVISORS: COMMITTEE MEMBERS: MPACT Status: Incomplete - Not_Inspected Title: Ribonucleic acid architecture dictates its binding and catalytic properties Abstract: Research in Ribonucleic acid (RNA) chemistry has grown dramatically with the recognition that RNA can act as enzymes as well as genetic carrier. Yet a lot remains to be known about how RNA utilizes its limited building blocks to manifest diverse structural motifs to support catalysis. The current work addresses two aspects of RNA catalysis: substrate binding and the link between folding and catalytic mechanisms. RNA binding motifs (aptamers) have been selected for flavin adenine dinucleotide (FAD), an essential redox cofactor, from a library of RNA molecules (∼ 1 x 10 15 different species) using in vitro selection-amplification process. Distinct RNA architectures were obtained under two different selection conditions: a stem-loop structure and a three-way helical junction structure. Secondary structure of the first aptamer was investigated using comparative sequence analysis, mutational analysis and enzymatic foot-printing. The secondary structure of the second class of aptamers was obtained from comparative sequence analysis and modeling using MFOLD software. Although the first aptamer recognized the redox center of flavin, yet it was unable to differentiate between the two redox forms of FAD but the second aptamer was able to differentiate between FAD and FADH 2 based on relative binding assays. |
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